Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Now showing 1 - 8 of 8
  • Master Thesis
    Molecular Investigation of P. Aeruginosa in the Presence of 4-Hba
    (01. Izmir Institute of Technology, 2023) Ekenel, Nil Hazal; Soyer Dönmez, Ferda
    The escalating threat to human health posed by bacterial pathogens is increasingly attributed to the growing prevalence and distribution of antibiotic-resistant bacteria. In response to antibiotics, microorganisms have developed resistance mechanisms to elude and survive the impacts of these drugs. Phenolic acids have emerged as potent candidates in the battle against bacterial infections due to their unique property of not inducing resistance. This study focuses explicitly on 4-hydroxybenzoic acid (4-HBA), a type of phenolic acid, as an effective antimicrobial agent. Proteomics research has become an indispensable tool in the fight against antimicrobial resistance. Pseudomonas aeruginosa, a bacterium capable of existing in both planktonic and biofilm states and known to cause numerous human diseases, is of particular significance in this context. Furthermore, the study explores the molecular aspects of P. aeruginosa when exposed to 4-HBA through proteomic analysis, revealing a significant impact on protein biosynthesis as a predominantly affected function. Additionally, P. aeruginosa, the study investigates the effects of phenolic acid and antibiotic-loaded bone cements on Methicillin-sensitive Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecium, and P. aeruginosa. Remarkably, 20 percent inhibition rate is achieved after 48 hours of treatment. Moreover, the study examines biofilm produced by P. aeruginosa in the presence of 4-HBA, utilizing both the Crystal Violet assay and Scanning Electron Microscopy. Significantly, the biofilm formation is observed to be disrupted by these methodologies. Overall, this study underscores the effectiveness of 4-HBA as antimicrobial compound against diverse range of pathogens, as demonstrated through both phenotypic and proteomic approaches.
  • Master Thesis
    Mass Spectrometry-Based Proteome Analysis of Leishmania Major Parasite in Two Clinical Isolates Which Exhibit Different Impact on Virulence
    (Izmir Institute of Technology, 2018) Güvenç, Nazlı; Yalçın, Talat
    Leishmaniasis is a disease that covered under the title of neglected tropical diseases caused by protozoan parasites called Leishmania which can classify into three groups as visceral, cutaneous and mucocutaneous leishmaniasis. L. major is a type of parasite that causes cutaneous leishmaniasis and it is endemic in Iran, and Syria. However, cutaneous type leishmaniasis caused by L. major has been begun to detect in Turkey due to its close location to such countries. Moreover, the variety in the infectivity of L. major in a different region of Turkey has detected. Therefore, the uncertainty under the virulence effect of L. major is aimed to investigate. Large-scale protein analysis by mass spectrometry based proteomics has cleared up to proteome mapping for different organism recently. Generally, although two methodologies that involve gel-free and gel-based approaches have widely accepted for proteomic analysis, gel-free LC-MS/MS analysis were applied to characterize the proteome analysis of L. major parasite in two clinical case exhibiting passive and aggressive virulence effect on leishmaniasis. Finally, differential and common proteins that can affect the infectivity of L. major invastigated by shotgun analysis. As a result, samples showed that there are conflict results with the literature about GP63, secreted acid proteases, cysteine proteases and Peroxiredoxin proteins existence and also in the aggressive L. major cystathionine beta-synthase protein which has an role to synthesis of CPs and pyridoxal phosphate binding activity were proposed as a critical protein for L. major infectivity due to its association with SAPs, CPs.
  • Master Thesis
    Mass Spectrometry-Based Comparative Proteomic Analysis of Drug Resistant and Nonresistant Strains of Parasite Trichomonas Vaginalis
    (Izmir Institute of Technology, 2018) Özyağcı, Begüm; Yalçın, Talat
    Trichomonas vaginalis (T. vaginalis) causes sexually transmitted disease, trichomoniasis. Acute infections can result in cervical cancer, pelvic inflammatory disease, HIV-1 infection, preterm births, and low birth weight. Metronidazole, an antibiotic, is the standard treatment of the disease. However, in some cases T. vaginalis shows resistance to metronidazole thus treatment fails. Nevertheless, resistance mechanism of the parasite is not fully understood. Mass spectrometry has become an important tool in proteomic analysis with the emergence of soft ionization techniques instead of traditional protein identification and sequencing methods. In this study, a comparative gel-free proteomic analysis based on mass spectrometry with soft ionization technology was performed in two sets for resistant and non-resistant strains of T. vaginalis parasite isolated from clinical cases. Total proteins were digested by in solution digestion method and separated with high pH reversed-phase liquid chromatography. After fractions were concatenated, each fraction of sample was analyzed by reversed-phase liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and proteins were identified by database search. Common and differential proteins between resistant and two sensitive trichomoniasis samples were compared according to their molecular function. Results indicate that ferredoxin 5 and hydroxyl amine reductase are differential proteins with iron-sulfur cluster binding activity identified for only resistant strain. Thioredoxin reductase, alcohol dehydrogenase, superoxide dismutase, pyruvate:ferredoxin oxidoreductase are studied proteins in the literature and also identified as common proteins in all strains for this study. These proteins might have a role in drug resistance mechanism of T. vaginalis.
  • Master Thesis
    Importance of Database Normalization for Reliable Protein Identification in Mass Spectrometry-Based Proteomics
    (Izmir Institute of Technology, 2016) Mungan, Mehmet Direnç; Allmer, Jens; Yalçın, Talat
    One of the revolutionary steps towards proteomics, was introducing mass spectrometry to protein inference analysis. Its powerful aspects such as speed, and accuracy towards identifying and quantifying proteins have made it the first choice to obtain highthroughput data. Due to development of a variety of fragmentation techniques, mass spectrometry-based analysis even made it possible to acquire knowledge about single polymorphisms and modifications of amino acids of a peptide. Although this technology provides enormous amounts of data, identification of the proteins is still a hard challenge to overcome due to the shortcomings of computational methods. Herein a novel methodology is offered to better analyze mass spectrometry data and overcome the deficiency of protein identification algorithms in terms of speed and accuracy. When the spectral data is acquired from an organism by mass spectrometry, database search algorithms are used for protein identification if the protein sequences of the organism are known. These algorithms compare the experimental data from mass spectrometry analysis to theoretical data gathered from known databases of organism to try and find the best match by ranking the PSMs via scoring functions. Since the databases can be too large to search and multiple databases with different sizes can contain the peptides of experimental data, database search algorithms may fail to produce fair, fast or complete results. In this work a methodology is presented to overcome unfair scoring of peptides in different size databases and enable database search algorithms to utilize relatively big sized entries such as human chromosome six frame translations. In terms of speed and accuracy the method is found to be better than some of the existing methods.
  • Master Thesis
    Ray: a Profile-Based Approach for Homology Matching of Tandem-Ms Spectra To Sequence Databases
    (Izmir Institute of Technology, 2012) Yılmaz, Şule; Allmer, Jens; Karaçalı, Bilge
    Mass spectrometry is a tool that is commonly used in proteomics to identify and quantify proteins. Thousands of spectra can be obtained in just few hours. Computational methods enable the analysis of high-throughput studies. There are mainly two strategies: database search and de novo sequencing. Most of the researchers prefer database search as a first choice but any slight changes on protein can prevent identification. In such cases, de novo sequencing can be used. However, this approach highly depends on spectral quality and it is difficult to achieve predictions with full length sequence. Peptide sequence tags (PST) allows some flexibility on database searches. A PST is a short amino acid sequence with certain mass information but obtaining accurate PST is still arduous. In case a sequence is missing in database, homology searches can be useful. There are some homology search algorithms such as MS-BLAST, MS-Shotgun, FASTS. But, they are altered versions of existing algorithms, for example BLAST has been modified for mass spectrometric data and became MS-BLAST. Besides, they are usually coupled with de novo sequencing which still possess limitations. Therefore, there is a need for novel algorithms in order to increase the scope of homology searches. For this purpose, a novel approach that is based on sequence profiles has been implemented. A sequence profile is like a table that contains frequencies of all possible amino acids on a given MS/MS spectrum. Then, they are aligned to sequences in database. Profiles are more specific than PSTs and the requirement for precursor mass restrictions or enzyme information can be removed.
  • Master Thesis
    Changes in Protein Profiles in Bortezomib Applied Multiple Myeloma Cells
    (Izmir Institute of Technology, 2011) Turan, Taylan; Şanlı Mohamed, Gülşah
    Multiple Myeloma is a malignant B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. Over the recent years, several novel agents have been introduced in the treatment of this disease. Bortezomib is the first of a new class of agents known as proteasome inhibitors. The main objective of the project was basically to both determine the cytotoxic and apoptotic effects of Bortezomib on Multiple Myeloma U-266 cells and compare and explore the differences between Bortezomib applied Multiple Myeloma cells and control group Multiple Myeloma cells, by proteomics studies. In order to achieve our aims in the project, variety of multidisciplinary subjects were come together. Cancer research techniques, biochemical studies at protein level and proteomics were combined in our studies. In this study, our experimental results demonstrated that Bortezomib has antiproliferative and apoptotic effects on MM U-266 cells. On the other hand, the responsible proteins for the effect mechanism of anti-cancer agent on cells were determined by MALDI-TOF-TOF Mass Spectrometry for the first time. According to the mass spectrometric analysis, 37 protein spots were differentially expressed. Among them, five proteins were newly formed, ten proteins lost, twelve proteins were up-regulated and ten proteins were down-regulated as compared to control group (untreated cells).These differential expressed proteins in response to Bortezomib have different important functions ranging from cell signaling transduction, cell cycle regulation, apoptosis to immunity and defense mechanism. In conclusion, it was identified which proteins have a central role behind the effect of Bortezomib on MM U-266 cells. The identified proteins may let to be possible to treat other cancer types by same anticancer agent. The data obtained by this study may also be helpful for medical schools and drug designers and may also provide new treatments.
  • Master Thesis
    Proteomic Analysis of Boron Stress Response in Yeast Saccharomyces Cerevisiale
    (Izmir Institute of Technology, 2011) Avşar, Kadir; Koç, Ahmet
    Boron is a versatile element distributed in every part of the environment but most of its deposit reserves are localized in a few countries, Turkey being one of the most prominent. Boron is known to be an essential micronutrient for plants and some animals. Like any other essential element it has toxicity in high concentrations. Herein the mechanism of toxicity and the elements of the boron stress response were investigated in Saccharomyces cerevisiae with a proteomics approach. Boron is believed to have played a role in the evolution of life on earth. It has strongly electrophile organic compounds, the most important physiological form being boric acid. Boric acid has a capacity to bind cis-located hydroxl groups and some amino groups. Some of these groups are located at the active sites of some enzymes and at the carbohydrates with five-membered furanose rings. The riboses of some metabolically important molecules like S-adenosyl methionine, diadenosine phosphate family members and 3'end of RNAs are prone to be affected. The yeast cells subjected to boron in this study expressed higher amounts of carbohydrate metabolic enzymes, proteins involved in protein synthesis, protein folding and catabolism, redox homeostasis and nucleotide synthesis. All of these proteins are common to metal stress responses in yeasts. Some of them involve in other stress responses like peroxide, salt or herbicide stresses showing complex interplay between responses.
  • Master Thesis
    Exploiting Fragment-Ion Complementarity for Peptide De Novo Sequencing From Collision Induced Dissociation Tandem Mass Spectra
    (Izmir Institute of Technology, 2011) Aytun, Belgin; Allmer, Jens
    Peptide identification from mass spectrometric data is a key step in proteomics because this field provides sequence, quantitative, and modification data of actually expressed proteins. Two approaches are generally deployed to interpret experimental MS/MS data, database searching and de novo sequencing. Database search method has been used successfully in proteomics projects for organisms with well-studied genomes. However, it is not applicable in situations where a target sequence is not in the protein database. This can happen for a number of reasons, including novel proteins, protein mutations and post-translational modifications. Because of the disadvantages of database searching method, a lot of research has focused on de novo sequencing method which assigns amino acid sequences to MS/MS spectra without the need for a database. The aim of this study is to enhance the accuracy of de novo sequencing tools. One step commonly employed in all de novo sequencing tools is naming of fragment ions. It is essential to know which peak represents which ion type in order to traverse a spectrum graph to find an amino acid sequence that best explains the MS/MS spectrum. Different approaches have been tried to name ions and some success has been achieved in naming b-type ions and y-type ions. We have presented a new approach which enables the naming of not only b- and y-type ions but other arbitrary ion types as well. This enabled the detection of b-ion ladder. In the latter case, missing fragments were determined by using other named ion types. Furthermore, unexplained data in tandem mass spectra were reduced as much as possible. Therefore, a complete sequence will be derived by the new approach.